Biofilms for Production of Chemicals and Energy

The twenty-first century will be the century of biology. This is not only because of breakthrough advances in molecular biology tools but also because we need to reinvent our economy based on the biological principles of energy efficiency and sustainability. Consequently, new tools for production routines must be developed to help produce platform chemicals and energy sources based on sustainable resources. In this context, biofilm-based processes have the potential to impact future production processes, because they can be carried out continuously and with robust stationary biocatalysts embedded in an extracellular matrix with different properties. We review productive biofilm systems used for heterotrophic and lithoautotrophic production and attempt to identify fundamental reasons why they may be particularly suitable as future production systems.

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al. J. Am. Chem. Soc. 142, 10459-10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. We here explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck-Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

Genetic Engineering of Microorganisms with Electroactive Genes for the Fabrication of Electrochemical Microbial Biosensors

By integrating electroactive genes into engineered sensing microorganisms, information about the object to be measured can be converted into the output of an electrical signal, omitting the process of converting the output of an electrical signal in conventional sensing strategies and simplifying the steps of biosensor development. By utilizing synthetic biology methods, we can not only create novel genetic circuits by using logic gate operations and integrating genes from other biological components, solving biosensing issues in living systems and enhancing sensor performance, but also convert various types of genetic circuits into electrical signals, broadening the application range of biosensors. Here, we describe an example of how to genetically engineer microorganisms with electroactive genes and the fabrication of an electrochemical microbial biosensor.

In Situ Enhanced Yields of Microbial Nanowires: The Key Role of Environmental Stress

The conductive microbial nanowires of Geobacter sulfurreducens serve as a model for long-range extracellular electron transfer (EET), which is considered a revolutionary "green" nanomaterial in the fields of bioelectronics, renewable energy, and bioremediation. However, there is no efficient pathway to induce microorganisms to express a large amount of microbial nanowires. Here, several strategies have been used to successfully induce the expression of microbial nanowires. Microbial nanowire expression was closely related to the concentration of electron acceptors. The microbial nanowire was around 17.02 μm in length, more than 3 times compared to its own length. The graphite electrode was used as an alternative electron acceptor by G. sulfurreducens, which obtained a fast start-up time of 44 h in microbial fuel cells (MFCs). Meanwhile, Fe(III) citrate-coated sugarcane carbon and biochar were prepared to test the applicability of these strategies in the actual microbial community. The unsatisfied EET efficiency between c-type cytochrome and extracellular insoluble electron receptors promoted the expression of microbial nanowires. Hence, microbial nanowires were proposed to be an effective survival strategy for G. sulfurreducens to cope with various environmental stresses. Based on this top-down strategy of artificially constructed microbial environmental stress, this study is of great significance for exploring more efficient methods to induce microbial nanowires expression.

Nanomaterials in bioelectrochemical devices: on applications enhancing their positive effect

Electrochemical biosensors and biofuel cells are finding an ever-increasing practical application due to several advantages. Biosensors are miniature measuring devices, which can be used for on-the-spot analyses, with small assay times and sample volumes. Biofuel cells have dual benefits of environmental cleanup and electric energy generation. Application of nanomaterials in biosensor and biofuel-cell devices increases their functioning efficiency and expands spheres of use. This review discusses the potential of nanomaterials in improving the basic parameters of bioelectrochemical systems, including the sensitivity increase, detection lower-limit decrease, detection-range change, lifetime increase, substrate-specificity control. In most cases, the consideration of the role of nanomaterials links a certain type of nanomaterial with its effect on the bioelectrochemical device upon the whole. The review aims at assessing the effects of nanomaterials on particular analytical parameters of a biosensor/biofuel-cell bioelectrochemical device.

Biomaterials and Electroactive Bacteria for Biodegradable Electronics

The global production of unrecycled electronic waste is extensively growing each year, urging the search for alternatives in biodegradable electronic materials. Electroactive bacteria and their nanowires have emerged as a new route toward electronic biological materials (e-biologics). Recent studies on electron transport in cable bacteria—filamentous, multicellular electroactive bacteria—showed centimeter long electron transport in an organized conductive fiber structure with high conductivities and remarkable intrinsic electrical properties. In this work we give a brief overview of the recent advances in biodegradable electronics with a focus on the use of biomaterials and electroactive bacteria, and with special attention for cable bacteria. We investigate the potential of cable bacteria in this field, as we compare the intrinsic electrical properties of cable bacteria to organic and inorganic electronic materials. Based on their intrinsic electrical properties, we show cable bacteria filaments to have great potential as for instance interconnects and transistor channels in a new generation of bioelectronics. Together with other biomaterials and electroactive bacteria they open electrifying routes toward a new generation of biodegradable electronics.

Bio-electrochemical frameworks governing microbial fuel cell performance: technical bottlenecks and proposed solutions

Microbial fuel cells (MFCs) are recognized as a future technology with a unique ability to exploit metabolic activities of living microorganisms for simultaneous conversion of chemical energy into electrical energy. This technology holds the promise to offer sustained innovations and continuous development towards many different applications and value-added production that extends beyond electricity generation, such as water desalination, wastewater treatment, heavy metal removal, bio-hydrogen production, volatile fatty acid production and biosensors. Despite these advantages, MFCs still face technical challenges in terms of low power and current density, limiting their use to powering only small-scale devices. Description of some of these challenges and their proposed solutions is demanded if MFCs are applied on a large or commercial scale. On the other hand, the slow oxygen reduction process (ORR) in the cathodic compartment is a major roadblock in the commercialization of fuel cells for energy conversion. Thus, the scope of this review article addresses the main technical challenges of MFC operation and provides different practical approaches based on different attempts reported over the years.

Sustainable operation requires addressing key MFC-bottleneck issues. Enhancing extracellular electron transfer is the key to elevated MFC performance.

Electrical properties of outer membrane extensions from Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a metal-reducing bacterium that is able to exchange electrons with solid-phase minerals outside the cell. These bacterial cells can produce outer membrane extensions (OMEs) that are tens of nanometers wide and several microns long. The capability of these OMEs to transport electrons is currently under investigation. Tubular chemically fixed OMEs from S. oneidensis have shown good dc conducting properties when measured in an air environment. However, no direct demonstration of the conductivity of the more common bubble-like OMEs has been provided yet, due to the inherent difficulties in measuring it. In the present work, we measured the electrical properties of bubble-like OMEs in a dry air environment by Scanning Dielectric Microscopy (SDM) in force detection mode. We found that at the frequency of the measurements (∼2 kHz), OMEs show an insulating behavior, with an equivalent homogeneous dielectric constant ε_OME = 3.7 ± 0.7 and no dephasing between the applied ac voltage and the measured ac electric force. The dielectric constant measured for the OMEs is comparable to that obtained for insulating supramolecular protein structures (ε_protein = 3-4), pointing towards a rich protein composition of the OMEs, probably coming from the periplasm. Based on the detection sensitivity of the measuring instrument, the upper limit for the ac longitudinal conductivity of bubble-like OMEs in a dry air environment has been set to σ_OME,ac < 10^-5 S m^-1, a value several orders of magnitude smaller than the dc conductivity measured in tubular chemically fixed OMEs. The lack of conductivity of bubble-like OMEs can be attributed to the relatively large separation between cytochromes in these larger OMEs and to the suppression of cytochrome mobility due to the dry environmental conditions.

Desulfovibrio feeding Methanobacterium with electrons in conductive methanogenic aggregates from coastal zones

Geobacter, as a typical electroactive microorganism, is the "engine" of interspecies electron transfer (IET) between microorganisms. However, it does not have a dominant position in all natural environments. It is not known what performs a similar function as Geobacter in coastal zones. Metagenomic and metatranscriptomic analysis revealed that Desulfovibrio and Methanobacterium species were the most abundant in electrochemically active aggregates. Metatranscriptomic analysis showed that Desulfovibrio species highly expressed genes for ethanol metabolism and extracellular electron transfer involving cytochromes, pili and flagella. Methanobacterium species in the aggregates also expressed genes for enzymes involved in reducing carbon dioxide to methane. Pure cultures demonstrated that the isolated Desulfovibrio sp. strain JY contributed to aggregate conductivity and directly transferred electrons to Methanothrix harundinacea, which is unable to use H₂ or formate. Most importantly, further coculture studies indicated that Methanobacterium strain YSL might directly accept electrons from the Desulfovibrio strain JY for the reduction of carbon dioxide to methane in the aggregate. This finding suggested that the possibility of DIET by Desulfovibrio similar to Geobacter species in conductive methanogenic aggregates can not be excluded.

Acidophilic Iron- and Sulfur-Oxidizing Bacteria, Acidithiobacillus ferrooxidans, Drives Alkaline pH Neutralization and Mineral Weathering in Fe Ore Tailings

The neutralization of strongly alkaline pH conditions and acceleration of mineral weathering in alkaline Fe ore tailings have been identified as key prerequisites for eco-engineering tailings-soil formation for sustainable mine site rehabilitation. Acidithiobacillus ferrooxidans has great potential in neutralizing alkaline pH and accelerating primary mineral weathering in the tailings but little information is available. This study aimed to investigate the colonization of A. ferrooxidans in alkaline Fe ore tailings and its role in elemental sulfur (S⁰) oxidation, tailings neutralization, and Fe-bearing mineral weathering through a microcosm experiment. The effects of biological S⁰ oxidation on the weathering of alkaline Fe ore tailings were examined via various microspectroscopic analyses. It is found that (1) the A. ferrooxidans inoculum combined with the S⁰ amendment rapidly neutralized the alkaline Fe ore tailings; (2) A. ferrooxidans activities induced Fe-bearing primary mineral (e.g., biotite) weathering and secondary mineral (e.g., ferrihydrite and jarosite) formation; and (3) the association between bacterial cells and tailings minerals were likely facilitated by extracellular polymeric substances (EPS). The behavior and biogeochemical functionality of A. ferrooxidans in the tailings provide a fundamental basis for developing microbial-based technologies toward eco-engineering soil formation in Fe ore tailings.

Electrogenic and hydrocarbonoclastic biofilm at the oil-water interface as microbial responses to oil spill

The oil-water interface formed during an oil spill represents a challenging environment for pelagic communities living in aquatic ecosystems. At this anoxic barrier, we report the formation of a microbial hydrocarbonoclastic biofilm capable of electron transfer along the water column. This biofilm generated a membrane of surface-active compounds that allowed the spontaneous separation of electrical charges, causing the establishment of an anodic and a cathodic region and, as a result, the spontaneous creation of a liquid microbial fuel cell. Such floating biofilm was connected to the water column underneath by floating filaments that could contribute to oxygen reduction at distance. The filaments revealed an unusual lipid content induced by anoxic conditions, with prominent ultrastructural features similar to myelin found in oligodendrocytes of the vertebrate nervous system. Furthermore, these filaments showed an interesting cross-reactivity towards different epitopes of the myelin basic protein (MBP) and Claudin 11 (O₄) of human oligodendrocytes. The presence of a network of filaments similar to myelin suggests the probable existence of evolutionary connections between very distant organisms. Collectively these results suggest a possible mechanism for how lake microbial communities can adapt to oil spills while offering an interesting starting point for technological developments of liquid microbial fuel cells related to the study of hydrocarbon-water interfaces. The data that support the findings of this study are openly available in figshare at https://figshare.com/s/72bc73ae14011dc7920d.

Putative Extracellular Electron Transfer in Methanogenic Archaea

It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H₂ or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.

Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration

In nature as well as in industrial microbiology, all microorganisms need to achieve redox balance. Their redox state and energy conservation highly depend on the availability of a terminal electron acceptor, for example oxygen in aerobic production processes. Under anaerobic conditions in the absence of an electron acceptor, redox balance is achieved via the production of reduced carbon-compounds (fermentation). An alternative strategy to artificially stabilize microbial redox and energy state is the use of anodic electro-fermentation (AEF). This emerging biotechnology empowers respiration under anaerobic conditions using the anode of a bioelectrochemical system as an undepletable terminal electron acceptor. Electrochemical control of redox metabolism and energy conservation via AEF can steer the carbon metabolism towards a product of interest and avoid the need for continuous and cost-inefficient supply of oxygen as well as the production of mixed reduced by-products, as is the case in aerobic production and fermentation processes, respectively. The great challenge for AEF is to establish efficient extracellular electron transfer (EET) from the microbe to the anode and link it to central carbon metabolism to enhance the synthesis of a target product. This article reviews the advantages and challenges of AEF, EET mechanisms, microbial energy gain, and discusses the rational choice of substrate-product couple as well as the choice of microbial catalyst. Besides, it discusses the potential of the industrial model-organism Bacillus subtilis as a promising candidate for AEF, which has not been yet considered for such an application. This prospective review contributes to a better understanding of how industrial microbiology can benefit from AEF and analyses key-factors required to successfully implement AEF processes. Overall, this work aims to advance the young research field especially by critically revisiting the fundamental aspects of AEF.

Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation

The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.

Methanogenesis inhibitors used in bio-electrochemical systems: A review revealing reality to decide future direction and applications

Microbial fuel cell (MFC) is a robust technology capable of treating real wastewaters by utilizing mixed anaerobic microbiota as inoculum for producing electricity from oxidation of the biodegradable matters. However, these mixed microbiota comprises of both electroactive microorganisms (EAM) and substrate/electron scavenging microorganisms such as methanogens. Hence, in order to maximize bioelectricity from MFC, different physio-chemical techniques have been applied in past investigations to suppress activity of methanogens. Interestingly, recent investigations exhibit that methanogens can produce electricity in MFC and possess the cellular machinery like cytochrome c and Type IV pili to perform extracellular electron transfer (EET) in the presence of suitable electron acceptors. Hence, in this review, in-depth analysis of versatile behaviour of methanogens in both MFC and natural anaerobic conditions with different inhibition techniques is explored. This review also discusses the future research directions based on the latest scientific evidence on role of methanogens for EET in MFC.

Bacterial Flagellum versus Carbon Nanotube: A Review Article on the Potential of Bacterial Flagellum as a Sustainable and Green Substance for the Synthesis of Nanotubes

Bacterial flagella are complex multicomponent structures that help in cell locomotion. It is composed of three major structural components: the hook, the filament and basal body. The special mechanical properties of flagellar components make them useful for the applications in nanotechnology especially in nanotube formation. Carbon nanotubes (CNTs) are nanometer scale tube-shaped material and it is very useful in many applications. However, the production of CNTs is costly and detrimental to the environment as it pollutes the environment. Therefore, bacterial flagella have become a highly interesting research area especially in producing bacterial nanotubes that could replace CNTs. In this review article, we will discuss about bacterial flagellum and carbon nanotubes in the context of their types and applications. Then, we will focus and review on the characteristics of bacterial flagellum in comparison to carbon nanotubes and subsequently, the advantages of bacterial flagellum as nanotubes in comparison with carbon nanotubes.

Electroactive biofilms on surface functionalized anodes: The anode respiring behavior of a novel electroactive bacterium, Desulfuromonas acetexigens

Surface chemistry is known to influence the formation, composition, and electroactivity of electron-conducting biofilms. However, understanding of the evolution of microbial composition during biofilm development and its impact on the electrochemical response is limited. Here we present voltammetric, microscopic and microbial community analysis of biofilms formed under fixed applied potential for modified graphite electrodes during early (90 h) and mature (340 h) growth phases. Electrodes modified to introduce hydrophilic groups (-NH₂, -COOH and -OH) enhance early-stage biofilm formation compared to unmodified or electrodes modified with hydrophobic groups (-C₂H₅). In addition, early-stage films formed on hydrophilic electrodes are dominated by the gram-negative sulfur-reducing bacterium Desulfuromonas acetexigens while Geobacter sp. dominates on -C₂H₅ and unmodified electrodes. As biofilms mature, current generation becomes similar, and D. acetexigens dominates in all biofilms irrespective of surface chemistry. Electrochemistry of pure culture D. acetexigens biofilms reveal that this microbe is capable of forming electroactive biofilms producing considerable current density of > 9 A/m² in a short period of potential-induced growth (~19 h following inoculation) using acetate as an electron donor. The inability of D. acetexigens biofilms to use H₂ as a sole source electron donor for current generation shows promise for maximizing H₂ recovery in single-chambered microbial electrolysis cell systems treating wastewaters.

Protein Nanowires: the Electrification of the Microbial World and Maybe Our Own

Electrically conductive protein nanowires appear to be widespread in the microbial world and are a revolutionary "green" material for the fabrication of electronic devices. Electrically conductive pili (e-pili) assembled from type IV pilin monomers have independently evolved multiple times in microbial history as have electrically conductive archaella (e-archaella) assembled from homologous archaellin monomers. A role for e-pili in long-range (micrometer) extracellular electron transport has been demonstrated in some microbes. The surprising finding of e-pili in syntrophic bacteria and the role of e-pili as conduits for direct interspecies electron transfer have necessitated a reassessment of routes for electron flux in important methanogenic environments, such as anaerobic digesters and terrestrial wetlands. Pilin monomers similar to those found in e-pili may also be a major building block of the conductive "cables" that transport electrons over centimeter distances through continuous filaments of cable bacteria consisting of a thousand cells or more. Protein nanowires harvested from microbes have many functional and sustainability advantages over traditional nanowire materials and have already yielded novel electronic devices for sustainable electricity production, neuromorphic memory, and sensing. e-pili can be mass produced with an Escherichia coli chassis, providing a ready source of material for electronics as well as for studies on the basic mechanisms for long-range electron transport along protein nanowires. Continued exploration is required to better understand the electrification of microbial communities with microbial nanowires and to expand the "green toolbox" of sustainable materials for wiring and powering the emerging "Internet of things."

Bacterial nanotubes mediate bacterial growth on periodic nano-pillars

Surface topography designed to achieve spatial segregation has shown promise in delaying bacterial attachment and biofilm growth. However, the underlying mechanisms linking surface topography to the inhibition of microbial attachment and growth still remain unclear. Here, we investigated bacterial attachment, cell alignment and biofilm formation of Pseudomonas aeruginosa on periodic nano-pillar surfaces with different pillar spacing. Using fluorescence and scanning electron microscopy, bacteria were shown to align between the nanopillars. Threadlike structures ("bacterial nanotubes") protruded from the majority of bacterial cells and appeared to link cells directly with the nanopillars. Using ΔfliM and ΔpilA mutants lacking flagella or pili, respectively, we further demonstrated that cell alignment behavior within nano-pillars is independent of the flagella or pili. The presence of bacteria nanotubes was found in all cases, and is not linked to the expression of flagella or pili. We propose that bacterial nanotubes are produced to aid in cell-surface or cell-cell connections. Nano-pillars with smaller spacing appeared to enhance the extension and elongation of bacterial nanotube networks. Therefore, nano-pillars with narrow spacing can be easily overcome by nanotubes that connect isolated bacterial aggregates. Such nanotube networks may aid cell-cell communication, thereby promoting biofilm development.

Genetic engineering for enhanced productivity in bioelectrochemical systems

A shift from petrochemical processes toward a bio-based economy is one of the most advocated developments for a sustainable future. To achieve this will require the biotechnological production of platform chemicals that can be further processed by chemical engineering. Bioelectrochemical systems (BESs) are a novel tool within the biotechnology field. In BESs, microbes serve as biocatalysts for the production of biofuels and value-added compounds, as well as for the production of electricity. Although the general feasibility of bioelectrochemical processes has been demonstrated in recent years, much research has been conducted to develop biocatalysts better suited to meet industrial demands. Initially, mainly natural exoelectrogenic organisms were investigated for their performance in BESs. Driven by possibilities of recent developments in genetic engineering and synthetic biology, the spectrum of microbial catalysts and their versatility (substrate and product range) have expanded significantly. Despite these developments, there is still a tremendous gap between currently achievable space-time yields and current densities on the one hand and the theoretical limits of BESs on the other. It will be necessary to move the performance of the biocatalysts closer to the theoretical possibilities in order to establish viable production routines. This review summarizes the status quo of engineering microbial biocatalysts for anode-applications with high space-time yields. Furthermore, we will address some of the theoretical limitations of these processes exemplarily and discuss which of the present strategies might be combined to achieve highly synergistic effects and, thus, meet industrial demands.

How does electron transfer occur in microbial fuel cells?

Microbial fuel cells (MFCs) have emerged as a promising technology for sustainable wastewater treatment coupled with electricity generation. A MFC is a device that uses microbes as catalysts to convert chemical energy present in biomass into electrical energy. Among the various mechanisms that drive the operation of a MFC, extracellular electron transfer (EET) to the anode is one of the most important. Exoelectrogenic bacteria can natively transfer electrons to a conducting surface like the anode. The mechanisms employed for electron transfer can either be direct transfer via conductive pili or nanowires, or mediated transfer that involves either naturally secreted redox mediators like flavins and pyocyanins or artificially added mediators like methylene blue and neutral red. EET is a mechanism wherein microorganisms extract energy for growth and maintenance from their surroundings and transfer the resulting electrons to the anode to generate current. The efficiency of these electron transfer mechanisms is dependent not only on the redox potentials of the species involved, but also on microbial oxidative metabolism that liberates electrons. Attempts at understanding the electron transfer mechanisms will boost efforts in giving rise to practical applications. This article covers the various electron transfer mechanisms involved between microbes and electrodes in microbial fuel cells and their applications.

Geobacter Protein Nanowires

The study of electrically conductive protein nanowires in Geobacter sulfurreducens has led to new concepts for long-range extracellular electron transport, as well as for the development of sustainable conductive materials and electronic devices with novel functions. Until recently, electrically conductive pili (e-pili), assembled from the PilA pilin monomer, were the only known Geobacter protein nanowires. However, filaments comprised of the multi-heme c-type cytochrome, OmcS, are present in some preparations of G. sulfurreducens outer-surface proteins. The purpose of this review is to evaluate the available evidence on the in vivo expression of e-pili and OmcS filaments and their biological function. Abundant literature demonstrates that G. sulfurreducens expresses e-pili, which are required for long-range electron transport to Fe (III) oxides and through conductive biofilms. In contrast, there is no definitive evidence yet that wild-type G. sulfurreducens express long filaments of OmcS extending from the cells, and deleting the gene for OmcS actually increases biofilm conductivity. The literature does not support the concern that many previous studies on e-pili were mistakenly studying OmcS filaments. For example, heterologous expression of the aromatic-rich pilin monomer of Geobacter metallireducens in G. sulfurreducens increases the conductivity of individual nanowires more than 5,000-fold, whereas expression of an aromatic-poor pilin reduced conductivity more than 1,000-fold. This more than million-fold range in nanowire conductivity was achieved while maintaining the 3-nm diameter characteristic of e-pili. Purification methods that eliminate all traces of OmcS yield highly conductive e-pili, as does heterologous expression of the e-pilin monomer in microbes that do not produce OmcS or any other outer-surface cytochromes. Future studies of G. sulfurreducens expression of protein nanowires need to be cognizant of the importance of maintaining environmentally relevant growth conditions because artificial laboratory culture conditions can rapidly select against e-pili expression. Principles derived from the study of e-pili have enabled identification of non-cytochrome protein nanowires in diverse bacteria and archaea. A similar search for cytochrome appendages is warranted. Both e-pili and OmcS filaments offer design options for the synthesis of protein-based "green" electronics, which may be the primary driving force for the study of these structures in the near future.

Metabolite Cross-Feeding between Rhodococcus ruber YYL and Bacillus cereus MLY1 in the Biodegradation of Tetrahydrofuran under pH Stress

Bacterial consortia are among the most basic units in the biodegradation of environmental pollutants. Pollutant-degrading strains frequently encounter different types of environmental stresses and must be able to survive with other bacteria present in the polluted environments. In this study, we proposed a noncontact interaction mode between a tetrahydrofuran (THF)-degrading strain, Rhodococcus ruber YYL, and a non-THF-degrading strain, Bacillus cereus MLY1. The metabolic interaction mechanism between strains YYL and MLY1 was explored through physiological and molecular studies and was further supported by the metabolic response profile of strain YYL, both monocultured and cocultured with strain MLY1 at the optimal pH (pH 8.3) and under pH stress (pH 7.0), through a liquid chromatography-mass spectrometry-based metabolomic analysis. The results suggested that the coculture system resists pH stress in three ways: (i) strain MLY1 utilized acid metabolites and impacted the proportion of glutamine, resulting in an elevated intracellular pH of the system; (ii) strain MLY1 had the ability to degrade intermediates, thus alleviating the product inhibition of strain YYL; and (iii) strain MLY1 produced some essential micronutrients for strain YYL to aid the growth of this strain under pH stress, while strain YYL produced THF degradation intermediates for strain MLY1 as major nutrients. In addition, a metabolite cross-feeding interaction with respect to pollutant biodegradation is discussed.IMPORTANCE Rhodococcus species have been discovered in diverse environmental niches and can degrade numerous recalcitrant toxic pollutants. However, the pollutant degradation efficiency of these strains is severely reduced due to the complexity of environmental conditions and limitations in the growth of the pollutant-degrading microorganism. In our study, Bacillus cereus strain MLY1 exhibited strong stress resistance to adapt to various environments and improved the THF degradation efficiency of Rhodococcus ruber YYL by a metabolic cross-feeding interaction style to relieve the pH stress. These findings suggest that metabolite cross-feeding occurred in a complementary manner, allowing a pollutant-degrading strain to collaborate with a nondegrading strain in the biodegradation of various recalcitrant compounds. The study of metabolic exchanges is crucial to elucidate mechanisms by which degrading and symbiotic bacteria interact to survive environmental stress.

Decorating the Outer Surface of Microbially Produced Protein Nanowires with Peptides

The potential applications of electrically conductive protein nanowires (e-PNs) harvested from Geobacter sulfurreducens might be greatly expanded if the outer surface of the wires could be modified to confer novel sensing capabilities or to enhance binding to other materials. We developed a simple strategy for functionalizing e-PNs with surface-exposed peptides. The G. sulfurreducens gene for the monomer that assembles into e-PNs was modified to add peptide tags at the carboxyl terminus of the monomer. Strains of G. sulfurreducens were constructed that fabricated synthetic e-PNs with a six-histidine "His-tag" or both the His-tag and a nine-peptide "HA-tag" exposed on the outer surface. Addition of the peptide tags did not diminish e-PN conductivity. The abundance of HA-tag in e-PNs was controlled by placing expression of the gene for the synthetic monomer with the HA-tag under transcriptional regulation. These studies suggest broad possibilities for tailoring e-PN properties for diverse applications.

The Archaellum of Methanospirillum hungatei Is Electrically Conductive

Microbially produced electrically conductive protein filaments are a revolutionary, sustainably produced, electronic material with broad potential applications. The design of new protein nanowires based on the known M. hungatei archaellum structure could be a major advance over the current empirical design of synthetic protein nanowires from electrically conductive bacterial pili. An understanding of the diversity of outer-surface protein structures capable of electron transfer is important for developing models for microbial electrical communication with other cells and minerals in natural anaerobic environments. Extracellular electron exchange is also essential in engineered environments such as bioelectrochemical devices and anaerobic digesters converting wastes to methane. The finding that the archaellum of M. hungatei is electrically conductive suggests that some archaea might be able to make long-range electrical connections with their external environment.

Microbially produced electrically conductive protein filaments are of interest because they can function as conduits for long-range biological electron transfer. They also show promise as sustainably produced electronic materials. Until now, microbially produced conductive protein filaments have been reported only for bacteria. We report here that the archaellum of Methanospirillum hungatei is electrically conductive. This is the first demonstration that electrically conductive protein filaments have evolved in Archaea. Furthermore, the structure of the M. hungatei archaellum was previously determined (N. Poweleit, P. Ge, H. N. Nguyen, R. R. O. Loo, et al., Nat Microbiol 2:16222, 2016, https://doi.org/10.1038/nmicrobiol.2016.222). Thus, the archaellum of M. hungatei is the first microbially produced electrically conductive protein filament for which a structure is known. We analyzed the previously published structure and identified a core of tightly packed phenylalanines that is one likely route for electron conductance. The availability of the M. hungatei archaellum structure is expected to substantially advance mechanistic evaluation of long-range electron transport in microbially produced electrically conductive filaments and to aid in the design of “green” electronic materials that can be microbially produced with renewable feedstocks.

Microbial nanowires - Electron transport and the role of synthetic analogues

Electron transfer is central to cellular life, from photosynthesis to respiration. In the case of anaerobic respiration, some microbes have extracellular appendages that can be utilised to transport electrons over great distances. Two model organisms heavily studied in this arena are Shewanella oneidensis and Geobacter sulfurreducens. There is some debate over how, in particular, the Geobacter sulfurreducens nanowires (formed from pilin nanofilaments) are capable of achieving the impressive feats of natural conductivity that they display. In this article, we outline the mechanisms of electron transfer through delocalised electron transport, quantum tunnelling, and hopping as they pertain to biomaterials. These are described along with existing examples of the different types of conductivity observed in natural systems such as DNA and proteins in order to provide context for understanding the complexities involved in studying the electron transport properties of these unique nanowires. We then introduce some synthetic analogues, made using peptides, which may assist in resolving this debate. Microbial nanowires and the synthetic analogues thereof are of particular interest, not just for biogeochemistry, but also for the exciting potential bioelectronic and clinical applications as covered in the final section of the review.

STATEMENT OF SIGNIFICANCE

Some microbes have extracellular appendages that transport electrons over vast distances in order to respire, such as the dissimilatory metal-reducing bacteria Geobacter sulfurreducens. There is significant debate over how G. sulfurreducens nanowires are capable of achieving the impressive feats of natural conductivity that they display: This mechanism is a fundamental scientific challenge, with important environmental and technological implications. Through outlining the techniques and outcomes of investigations into the mechanisms of such protein-based nanofibrils, we provide a platform for the general study of the electronic properties of biomaterials. The implications are broad-reaching, with fundamental investigations into electron transfer processes in natural and biomimetic materials underway. From these studies, applications in the medical, energy, and IT industries can be developed utilising bioelectronics.

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium

Trichodesmium spp. are diazotrophic cyanobacteria that exist as single filaments (trichomes) and as macroscopic colonies of varying shapes formed by aggregating trichomes. The causes and dynamics of colony formation and disassociation are not yet elucidated. we demonstrate that limited availability of dissolved phosphorus (P) or iron (Fe) stimulated trichome mobility and induced colony formation in Trichodesmium erythraeum IMS101 cultures. The specific nutrient limitation differentially affected the rate of colony formation and morphology of the colonies. Fe starvation promoted rapid colony formation (10-48 h from depletion) while 5-7 days were required for colonies to form in P-depleted cultures. Video analyses confirmed that the probability of trichomes to cluster increased from 12 to 35% when transferred from nutrient replete to Fe-depleted conditions. Moreover, the probability for Fe-depleted aggregates to remain colonial increased to 50% from only 10% in nutrient replete cultures. These colonies were also characterized by stronger attachment forces between the trichomes. Enrichment of nutrient-depleted cultures with the limited nutrient-stimulated colony dissociation into single trichomes. We postulate that limited P and Fe availability enhance colony formation of Trichodesmium and primarily control the abundance and distribution of its different morphologies in the nutrient-limited surface ocean.

Biophotovoltaics: Design and Study of Bioelectrochemical Systems for Biotechnological Applications and Metabolic Investigation

Biophotovoltaic methods rely on the fact that photosynthetic microorganisms, like many others, can export small amounts of electric current. For photosynthetic organisms, this current usually increases on illumination. This "exoelectrogenic" property may be of biotechnological interest, and may also provide useful experimental insights into the physiological status of the cell. We describe how to construct biophotovoltaic devices, and the kinds of measurements that are typically made.

e-Biologics: Fabrication of Sustainable Electronics with "Green" Biological Materials

The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new "green age" of sustainable electronic materials and devices.